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- PDB-1gtv: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINAS... -

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Entry
Database: PDB / ID: 1gtv
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE-5'-DIPHOSPHATE (TDP)
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE) / KINASE
Function / homology
Function and homology information


TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / THYMIDINE-5'-PHOSPHATE / THYMIDINE-5'-DIPHOSPHATE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.55 Å
AuthorsUrsby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Cryophotolysis of Caged Compounds: A Technique for Trapping Intermediate States in Protein Crystals
Authors: Ursby, T. / Weik, M. / Fioravanti, E. / Delarue, M. / Goeldner, M. / Bourgeois, D.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: X-Ray Structure of Tmp Kinase from Mycobacterium Tuberculosis Complexed with Tmp at 1.95 A Resolution
Authors: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Analysis of the Thymidylate Kinase from Mycobacterium Tuberculosis
Authors: De La Sierra Li, I. / Munier-Lehmann, H. / Gilles, A.M. / Barzu, O. / Delarue, M.
History
DepositionJan 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2002Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id ..._atom_site.label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02918
Polymers45,3252
Non-polymers1,70416
Water5,116284
1
A: THYMIDYLATE KINASE
hetero molecules

A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,10918
Polymers45,3252
Non-polymers1,78416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2180 Å2
ΔGint-9.7 kcal/mol
Surface area20830 Å2
MethodPQS
2
B: THYMIDYLATE KINASE
hetero molecules

B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94918
Polymers45,3252
Non-polymers1,62416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2180 Å2
ΔGint-9.6 kcal/mol
Surface area20810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.353, 76.353, 134.815
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2088-

HOH

DetailsNOTE THAT THE CRYSTAL CONTAINED 48% OF THE COMPLEX WITH TDP(TYD) AND 52% OF THE COMPLEX WITH TMP, WHICH IS REFLECTEDIN THE TWO MODELS IN THE STRUCTURE FILE. THE MODEL OF THECOMPLEX WITH TDP (TYD) IS OBTAINED BY TAKING CHAIN A, INCREASING THE OCCUPANCY BY A FACTOR 1/0.48 AND ADDING THEWATER MOLECULES WITH OCCUPANCY 1.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein THYMIDYLATE KINASE / / TMK


Mass: 22662.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O05891, UniProt: P9WKE1*PLUS, dTMP kinase

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Non-polymers , 6 types, 300 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: STARTING MODEL PDB ENTRY 1GSI
Crystal growpH: 6
Details: PROTEIN CRYSTALLIZED IN 1.4M AMMONIUM SULFATE,100MM MES PH6, 2% PEG 2000 25MM MAGNESIUM ACETATE,2MM BETA-MERCAPTOETHANOL, pH 6.00
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Li de La Sierra, I., (2000) Acta Crystallogr.,Sect., D56, 226.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.270-0.392 mMprotein1drop
22 mMdTMP1drop
31 mMdithiothreitol1drop
42 mMEDTA1drop
515 mMTris-HCl1droppH7.4
635 %ammonium sulfate1reservoir
72 %PEG20001reservoir
80.1 MMES1reservoirpH6.0
92 mMbeta-mercaptoethanol1reservoir
1025 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→25.3 Å / Num. obs: 33359 / % possible obs: 97.5 % / Redundancy: 10.8 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.2
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 9 / % possible all: 96
Reflection
*PLUS
Num. measured all: 360419
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.55→25.27 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 36-46, 73-81, 94 AND 159- 166 WERE MODELED IN A TYD CONFORMATION (CHAIN A), WHICH WAS REFINED, AND A TMP CONFORMATION (CHAIN B) TAKEN FROM PDB ENTRY 1GSI AND KEPT FIXED. THE REST OF ...Details: RESIDUES 36-46, 73-81, 94 AND 159- 166 WERE MODELED IN A TYD CONFORMATION (CHAIN A), WHICH WAS REFINED, AND A TMP CONFORMATION (CHAIN B) TAKEN FROM PDB ENTRY 1GSI AND KEPT FIXED. THE REST OF PROTEIN CHAINS A AND B WERE REFINED AND IDENTICAL FOR CHAINS A AND B. HET ATOMS AND WATER MOLECULES ANNOTATED AS CHAIN A OR B CORRESPOND TO THE TYD AND THE TMP CONFORMATIONS RESPECTIVELY, WITH THE TMP CONFORMATION ATOMS KEPT FIXED DURING REFINEMENT TO THE 1GSI COORDINATES.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1684 5 %RANDOM
Rwork0.192 ---
obs0.192 33350 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4639 Å2 / ksol: 0.353042 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å21.21 Å20 Å2
2--1.49 Å20 Å2
3----2.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 102 284 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.833.5
X-RAY DIFFRACTIONc_mcangle_it2.494
X-RAY DIFFRACTIONc_scbond_it2.614
X-RAY DIFFRACTIONc_scangle_it3.454.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 260 4.9 %
Rwork0.206 5092 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ACT.PARACT.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor obs: 0.206

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